The work aims to improve the production efficiency of package, elevate the stability, reliability and motion precision of the Cartesian coordinate robot, and plan the motion trajectory of the robot to avoid the sudden change of the robot's speed and acceleration. Firstly, the working principle of the Cartesian coordinate robot was analyzed. On the basis of this, cubic uniform B-spline curve was used to achieve the robot joint trajectory approximation. An optimal time B-spline trajectory planning method based on improved genetic algorithm was given. According to functional requirements, a control system based on ARM and FPGA was designed. The simulation results showed that, the robot joints reached the node with the shortest time, and the operation time could be reduced by 39%, and the effectiveness of the algorithm was verified. The proposed control system and method can meet the requirements of packaging and stacking, which can improve packaging efficiency.